[gmx-users] Number Density

Dear users, To calculate "Number Density" of solvent via size box for a bilayer membrane, I used g_density program as the following: g_density -f md.xtc -s md.tpr -o density-Num-SOL.xvg -d z -dens number -n index-group.ndx I got @    title "Partial densities" @    xaxis  label "Box (nm)" @    yaxi

[gmx-users] Atomtype OW not found

Hi, I am doing pure membrane simulation in DOPC environment (using Berger Lipids) in Gromacs 4.0.7  I want to try the grompp tool but have encountered this problem:   Fatal error: Atomtype OW  not found   Topology file is as the following: #include "lipid.itp" #include "dopc.itp" #include "spc.itp"

[gmx-users] Atomtype C not found

Hi   I have been using the lipids from Prof Tieleman's website and (using Berger Lipids) in gromacs 4.5.4  I want to try the grompp tool but have encountered this problem:   Fatal error: Atomtype C not found     Topology file is as the following: #include "lipid.itp" #include "dopc.itp" #include

[gmx-users] Membrane simulations

Dear all, I want to simulate DOPC membrane.I used the following site to find force field and topology files. http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies I have two questions: 1.This site design to simulate protein membrane not membrane. Should i use dopc.itp with lipid.